Genetic Variant CYP4F2:c.-1-22G>A (chr19-15897634-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001082.5(CYP4F2):c.-1-22G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00649 in 1,611,354 control chromosomes in the GnomAD database, including 486 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.029 ( 235 hom., cov: 31)

Exomes 𝑓: 0.0042 ( 251 hom. )

Consequence

CYP4F2
NM_001082.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.96

Publications

4 publications found

Variant links:

Genes affected

CYP4F2 (HGNC:2645): (cytochrome P450 family 4 subfamily F member 2) This gene encodes a member of the cytochrome P450 superfamily of enzymes. The cytochrome P450 proteins are monooxygenases which catalyze many reactions involved in drug metabolism and synthesis of cholesterol, steroids and other lipids. This protein localizes to the endoplasmic reticulum. The enzyme starts the process of inactivating and degrading leukotriene B4, a potent mediator of inflammation. This gene is part of a cluster of cytochrome P450 genes on chromosome 19. Another member of this family, CYP4F11, is approximately 16 kb away. [provided by RefSeq, Jul 2008]

CYP4F2 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.0).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0948 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CYP4F2	NM_001082.5 link	c.-1-22G>A		intron_variant	Intron 1 of 12	ENST00000221700.11	NP_001073.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CYP4F2	ENST00000221700.11 link	c.-1-22G>A		intron_variant	Intron 1 of 12	1	NM_001082.5	ENSP00000221700.3

Frequencies

GnomAD3 genomes

AF:

0.0287

AC:

4367

AN:

151980

Hom.:

230

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0969

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0101

Gnomad ASJ

AF:

0.0130

Gnomad EAS

AF:

0.00155

Gnomad SAS

AF:

0.00685

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.0158

Gnomad NFE

AF:

0.00116

Gnomad OTH

AF:

0.0188

GnomAD2 exomes

AF:

0.00954

AC:

2362

AN:

247694

AF XY:

0.00780

show subpopulations

Gnomad AFR exome

AF:

0.101

Gnomad AMR exome

AF:

0.00794

Gnomad ASJ exome

AF:

0.0134

Gnomad EAS exome

AF:

0.00180

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000928

Gnomad OTH exome

AF:

0.00973

GnomAD4 exome

AF:

0.00415

AC:

6060

AN:

1459256

Hom.:

251

Cov.:

AF XY:

0.00398

AC XY:

2890

AN XY:

725968

show subpopulations

African (AFR)

AF:

0.105

AC:

3501

AN:

33332

American (AMR)

AF:

0.00857

AC:

382

AN:

44568

Ashkenazi Jewish (ASJ)

AF:

0.0115

AC:

300

AN:

26050

East Asian (EAS)

AF:

0.000984

AC:

AN:

39652

South Asian (SAS)

AF:

0.00649

AC:

559

AN:

86164

European-Finnish (FIN)

AF:

0.0000191

AC:

AN:

52344

Middle Eastern (MID)

AF:

0.0114

AC:

AN:

5328

European-Non Finnish (NFE)

AF:

0.000545

AC:

606

AN:

1111562

Other (OTH)

AF:

0.0101

AC:

611

AN:

60256

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.454

Heterozygous variant carriers

225

450

675

900

1125

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

136

272

408

544

680

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0289

AC:

4392

AN:

152098

Hom.:

235

Cov.:

AF XY:

0.0282

AC XY:

2097

AN XY:

74380

show subpopulations

African (AFR)

AF:

0.0973

AC:

4032

AN:

41438

American (AMR)

AF:

0.0101

AC:

154

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.0130

AC:

AN:

3470

East Asian (EAS)

AF:

0.00136

AC:

AN:

5162

South Asian (SAS)

AF:

0.00644

AC:

AN:

4816

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10612

Middle Eastern (MID)

AF:

0.0170

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00116

AC:

AN:

68002

Other (OTH)

AF:

0.0186

AC:

AN:

2100

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.488

Heterozygous variant carriers

185

370

555

740

925

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

138

184

230

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0207

Hom.:

Bravo

AF:

0.0327

Asia WGS

AF:

0.0140

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.026

(source)

DANN

Benign

0.55

PhyloP100

-4.0

PromoterAI

-0.018

Neutral

(source)

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over